[RASMB] still Beckman software

[John Philo]

Kristian,

Sorry, I don't completely understand your question about that specific
simulation, but yes I believe the simulations are correct. They certainly
match quite closely what I see in real absorbance experiments, and that
simulator is very handy for planning equilibrium experiments.

You can ignore the whole units and conversion factors issue by simply
entering your loading concentrations in instrument units (fringes or
absorbance) and leaving the conversion factor at 1. If you do that the
simulated curves will be in instrument units also.

A simulation for 10 mg/ml of a 5 kDa molecule at 60K (assuming vbar = .73
and rho = 1) should not reach 250 fringes at the cell base. For such a
simulation I get about 150 fringes at the base, and ~30 fringes at a
location ~60% of the way down the cell, which should indeed be close to the
loading concentration of 33 fringes. If you are getting 250 fringes at the
cell base I suspect you did not change the mass from the default 68 kDa.

Also, regarding Jo Butler's comment, while he is certainly right that the
refractive increment is also wavelength dependent, I beg to differ with his
statement that the wavelength does not directly influence the fringes per
mg/ml conversion factor.

'Hope this helps,

John Philo

-----Original Message-----
From: rasmb-admin at server1.bbri.org
[mailto:rasmb-admin at server1.bbri.org]On Behalf Of Kristian Schilling
Sent: Tuesday, October 23, 2001 9:41 AM
To: rasmb at server1.bbri.org
Subject: [RASMB] RE: still Beckman software


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John,

have you actually seen this formula work quantitatively? In the sense,
perhaps, that the fringe number you get in the simulation actually matches
fringes measured for that material.

The factor of 3.3 you give would fit for 1,2 cm pieces, 675 nm light and
dn/dc = 0.190 ml/g, it would be in mg/ml. If I do a simulation with
meniscus depletion, say a 5000 Da species @ 60k, I get about 250 fringes at
the cell bottom for 10 mg/ml. There is no Ja here, so it is fairly easy to
calculate an initial loading concentration, which would be about 150
fringes. Such a sedimentation boundary would mean 44 mg/ml under the given
conditions. And not 10.

Either I am doing something terribly wrong or there is some additional
factor in there.

Kristian (not yet happy)

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